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(-) Description

Title :  CRYSTAL STRUCTURE OF SMAD5-MH1/PALINDROMIC SBE DNA COMPLEX
 
Authors :  N. Chai, J. Wang, Z. X. Wang, J. W. Wu
Date :  21 Feb 17  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Smad5, Mh1 Domain, Protein-Dna Complex, Sbe, Metal Binding Protein- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Chai, W. X. Li, J. Wang, Z. X. Wang, S. M. Yang, J. W. Wu
Structural Basis For The Smad5 Mh1 Domain To Recognize Different Dna Sequences.
Nucleic Acids Res. V. 43 9051 2015
PubMed-ID: 26304548  |  Reference-DOI: 10.1093/NAR/GKV848

(-) Compounds

Molecule 1 - MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MH1 DOMAIN (UNP RESIDUES 1-143)
    Gene: SMAD5, MADH5, MSMAD5
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MOTHERS AGAINST DPP HOMOLOG 5,DWARFIN-C,DWF-C,SMAD FAMILY MEMBER 5,MSMAD5
 
Molecule 2 - DNA (5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)- 3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)- 3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:65 , CYS A:110 , CYS A:122 , HIS A:127binding site for residue ZN A 201
2AC2SOFTWARECYS B:65 , CYS B:110 , CYS B:122 , HIS B:127binding site for residue ZN B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X6G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X6G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X6G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X6G)

(-) Exons   (0, 0)

(no "Exon" information available for 5X6G)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........eee......eee..eeehhhhhhhhhhh.....hhh.eee......hhhhh..eee.hhh.eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6g A  11 TSPAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSSPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLDICEFPFGSKQKEVCINPYHYKRVE 132
                                    20        30        40        50        60        70        80        90       100       110       120       130  


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........eee......eee..eeehhhhhhhhhhh.....hhh.eee.............eee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6g B  11 TSPAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSSPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLDICEFPFGSKQKEVCINPYHYKRVES 133
                                    20        30        40        50        60        70        80        90       100       110       120       130   


Chain C from PDB  Type:DNA  Length:15
                                               
                 5x6g C   1 ATCAGTCTAGACATA  15
                                    10     


Chain D from PDB  Type:DNA  Length:15
                                               
                 5x6g D   2 GTATGTCTAGACTGA  16
                                    11
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5X6G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X6G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X6G)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  SMAD5_MOUSE | P97454
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SMAD5_MOUSE | P97454: 5x6h 5x6m

(-) Related Entries Specified in the PDB File

5x6h 5x6m